Hi Andrew.
At first: I am also a newbie, so beware of my suggestions ;-)
Then I would suggest to install a newer version of bioperl. Bioperl is a
work in progress and you might miss some useful features or get some
bugs if you stick with bioperl 1.2.3. There is a simple way via CPAN
(just follow the instructions on www.bioperl.org) to update to 1.4. (But
I failed to update to 1.5 under windows, so I installed linux)
I think your problem is because there is no wrapper for btbblast. (at
least under 1.5)
Try blastall. Does it work?
Regards
Harald